Atomistry » Zinc » PDB 8d98-8dpo » 8dav
Atomistry »
  Zinc »
    PDB 8d98-8dpo »
      8dav »

Zinc in PDB 8dav: Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc)

Enzymatic activity of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc)

All present enzymatic activity of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc):
3.6.4.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc) (pdb code 8dav). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc), PDB code: 8dav:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8dav

Go back to Zinc Binding Sites List in 8dav
Zinc binding site 1 out of 2 in the Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn601

b:95.8
occ:1.00
 NE2 G:HIS139 2.0 63.5 1.0
SG G:CYS148 2.1 56.0 1.0
SG G:CYS137 2.2 78.0 1.0
SG G:CYS145 2.3 58.4 1.0
CD2 G:HIS139 2.8 63.5 1.0
CB G:CYS137 3.1 78.0 1.0
CE1 G:HIS139 3.1 63.5 1.0
N G:CYS145 3.3 58.4 1.0
CB G:CYS145 3.6 58.4 1.0
CB G:CYS148 3.7 56.0 1.0
CA G:CYS137 3.9 78.0 1.0
CG G:HIS139 4.0 63.5 1.0
CA G:CYS145 4.1 58.4 1.0
ND1 G:HIS139 4.1 63.5 1.0
CA G:MET144 4.2 52.2 1.0
C G:MET144 4.2 52.2 1.0
N G:CYS148 4.5 56.0 1.0
N G:GLU146 4.5 63.4 1.0
O G:GLY143 4.6 53.0 1.0
N G:TYR147 4.8 66.8 1.0
CA G:CYS148 4.8 56.0 1.0
N G:CYS137 4.8 78.0 1.0
C G:CYS145 4.8 58.4 1.0
CB G:MET144 4.9 52.2 1.0
C G:TYR147 5.0 66.8 1.0

Zinc binding site 2 out of 2 in 8dav

Go back to Zinc Binding Sites List in 8dav
Zinc binding site 2 out of 2 in the Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn602

b:89.7
occ:1.00
 NE2 G:HIS208 2.0 73.0 1.0
CE1 G:HIS208 2.1 73.0 1.0
SG G:CYS219 2.3 66.4 1.0
SG G:CYS216 2.3 61.1 1.0
SG G:CYS204 2.3 86.3 1.0
CB G:CYS219 3.0 66.4 1.0
N G:CYS216 3.1 61.1 1.0
CB G:CYS216 3.3 61.1 1.0
ND1 G:HIS208 3.4 73.0 1.0
CD2 G:HIS208 3.4 73.0 1.0
CA G:CYS216 3.7 61.1 1.0
CB G:CYS204 3.7 86.3 1.0
CG G:HIS208 4.0 73.0 1.0
C G:ILE215 4.1 56.1 1.0
CA G:CYS219 4.1 66.4 1.0
N G:CYS219 4.1 66.4 1.0
CA G:ILE215 4.2 56.1 1.0
C G:CYS216 4.4 61.1 1.0
O G:CYS216 4.6 61.1 1.0
O G:GLY207 4.8 84.7 1.0
CB G:ILE215 4.9 56.1 1.0
C G:CYS219 4.9 66.4 1.0
CG G:LYS218 5.0 76.5 1.0
CB G:ASN206 5.0 78.8 1.0

Reference:

H.G.Lee, A.A.Lemmon, C.D.Lima. UFD1 Interactions with Sumo Enhance Unfolding of Sumo-Polyubiquitin-Conjugated Substrates By the UFD1/NPL4/CDC48 Complex To Be Published.
Page generated: Fri Aug 22 09:11:27 2025

Last articles

Zn in 8SLF
Zn in 8SKT
Zn in 8SL1
Zn in 8SKP
Zn in 8SK2
Zn in 8SJC
Zn in 8SJG
Zn in 8SJH
Zn in 8SJB
Zn in 8SJ2
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy